This issue arises from the fact that mip count is handled differently in DdsFile and in DecodeInternal.

These are the relevent lines:
https://github.com/Nominom/BCnEncoder.NET/blob/master/BCnEnc.Net/Decoder/BcDecoder.cs#L1161-L1164
https://github.com/Nominom/BCnEncoder.NET/blob/master/BCnEnc.Net/Shared/ImageFiles/DdsFile.cs#L57

I think the easiest way to fix this would to be assume that each file has at least 1 mipmap. Microsoft says that you shouldn't rely on the mipmap flag being set.